Sequence
atgc intronic sequence ATGC exonic sequence...gtgcttgcttcactggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttactatgactggtggcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATAAAGTCTAGCAACATATTGATTGATACTGAGTTCAATGCAAAGGTTTCTG
Basic information
species | Glycine max |
transcript | GLYMA18G12830.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g35450.1 (Oryza sativa), 3'ss of exon 4
---------------gtgcttgcttcactggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttactat--gactggtg-gcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATAAAGTCTAGCAACATATTGATTGATACTGAGTTCAATGCAAAGGTTTCTG
| | ||| | |||| | | || | || | | || | | | ||| | || | | | | |||| |||||| ||||| ||||||||||||||||| || |||||||| ||||||||||| || || ||||||||| | || ||| || ||||||| || |||||
gtaagaaacaaaccatcgtccccgtcaaaaagaaaagaattgttcttcactttagctcttttat-atgtatatgtttagttgcataacccattttccataactgaattggtatacagGCTTGCTTATTTACATGAAGCAATAGAGCCAAAAGTTGTACACCGGGATATCAAATCAAGCAACATACTAATCGATGAAGAATTCAATGGCAAACTTTCT-
upper sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 4
gtgcttgcttcactggatacctaatttactgttatggcagtttcaacattaggccta-attccactgattaaactccttatttact--atgactggtggcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATAAAGTCTAGCAACATATTGATTGATACTGAGTTCAATGCAAAGGTTTCTG
| || ||| | | || || | || || || || || | ||| || | || | |||| |||||| ||||| ||||||||||| |||||||| |||||||| ||||| ||||| || |||||||| || | ||||| || ||||||| ||| |||||
---------gtaagacatggaccattcaatattttgtctcttctttgat---gcatatgttttgccatctaaggcatttttataattgatgatatactacagGCTTGCTTATTTACATGAAGCCATAGAACCAAAAGTTGTGCACCGTGATATCAAATCTAGCAATATCCTAGTTGATGAAGAATTCAATGGCAAGCTTTCT-
upper sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G017386_T03 (Zea mays), 3'ss of exon 4
gtgcttgcttca--ctggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttactatgactggtggcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATAAAGTCTAGCAACATATTGATTGATACTGAGTTCAATGCAAAGGTTTCTG
| | |||| || || ||| |||| || | | || || || | || || | || | | ||||| |||| ||||||| |||||| | |||||||| || || || |||||||| || || |||||||| || |||||||||||||||||| ||| || |||| || || |||
--gtaagtttcaatcttaatctgtaagttacctacatagtttcctgtgtttttagctgtataaaattggttcttattttt-ctaattatga-tggttgcagGCTTGCTTACCTTCATGAAGCTATTGAGCCAAAAGTTGTACATCGAGATATAAAATCAAGCAACATATTGATTGATGATGAATTTAATGGCAAAGTATCT-
upper sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G010953_T01 (Zea mays), 3'ss of exon 2
gtgcttgcttcactggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttacta-tgactggtg-gcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATAAAGTCTAGCAACATATTGATTGATACTGAGTTCAATGCAAAGGTTTCTG
| | || ||| ||| || || || || || | || || || | | | | | || || | ||| | ||| | |||||| ||||| ||||||||||| |||||||| |||||||| ||||| ||||| || || ||||| || || |||||| || ||||||| ||| |||||
------gtaagaaatgaaacc--attcacaattttg-catcttttatat---gcatacatttattaaattaagatgttgtctacaactgaacactatacagGCTTGCTTATTTACATGAAGCCATAGAACCAAAAGTTGTACACCGTGATATCAAATCGAGCAATATCTTAATTGATGAAGAATTCAATGGCAAGCTTTCT-
upper sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgcttgcttcactggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttactatgactggtggcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATAAAGTCTAGCAACATATTGATTGATACTGAGTTCAATGCAAAGGTTTCTG
|| || || | | | | | |||| | | ||||| || | ||| | | | | || | || || ||| | |||||| |||||||| ||||||||||||||||| ||||| || ||| | || ||||| | || || |||||||||||| |||||| |||||||| | |||
gtaagtggtttg--aaacagtttagcttttgttg-gatatgttcaat-----gcttgatt--attaaa-agggtctgcaatttgtacaact--ttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT-
upper sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgcttgcttcactggatacctaattta----ctgtta-tggcagtttcaacattaggcctaattccactgat-taaactccttatttactatgactggtggcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATAAAGTCTAGCAACATATTGATTGATACTGAGTTCAATGCAAAGGTTTCTG
|| | || | | || | | || ||| | | | |||||| | | || || ||| | || | | ||||| | | | |||||| ||||| |||||||||||||||||||| ||||| || ||| | || ||||| | ||||| || ||||||| ||| |||||||||||| |||||
gtaagttgtttaaaatgtgactgttgttggaccttttacttgaaatttcaaaaacaactct--ttaaggggatattgacatgctctgtactacaatt--ttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT-
upper sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 5
gtgcttgcttcactggatacctaatttactgttatggc--agtttcaacattaggcctaattccactgattaaactcctta----tttactatgactggtggcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATAAAGTCTAGCAACATATTGATTGATACTGAGTTCAATGCAAAGGTTTCTG
| | || | || || | | | | || ||||| | | |||| ||| | | | | || ||| ||||||| || || || ||||| ||||||||||||||||||||||| || || ||||| || |||||||| ||||||||| ||||||||||||||||||||||
-----tattccattcagaactgaaatctactccagaactgaaattgaacatcttggtctttcacactttgaaaaagtcaaaaaaatgtttcatattgggttgcagGCTTGCCTATTTGCATGAGGCAATAGAACCGAAAGTTGTTCATCGAGACATAAAATCAAGCAACATCTTGATTGATGATGAGTTCAATGCAAAGGTTTCT-Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|18730090|gb|BM525675.1|BM525675EST: CACTTACCTGGGAAGCTCGAATGAAAGTTATAACTGGAACAGCCAAAGCG CTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATA
genomic: CACTTACCTGGGAAGCTCGAATGAAAGTTATAACTGGAACAGCCAAAGCGtaagttctac ... tggtggcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATA
EST:
gi|192331429|gb|FK019902.1|FK019902EST: CACTTACCTGGGAAGCTCGAATGAAAGTTATAACTGGAACAGCCAAAGCG CTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATA
genomic: CACTTACCTGGGAAGCTCGAATGAAAGTTATAACTGGAACAGCCAAAGCGtaagttctac ... tggtggcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acattaggcctaattccactgattaaactccttatttactatgactggtggcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATAAAGTCTAGCAACATATTGATTGATACTGAGTTCAATGCAAAGGTTTCTG
cactgat putative branch site (score: 3)
ttatttactat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcttgcttcactggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttactatgactggtggcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATAAAGTCTAGCAACATATTGATTGATACTGAGTTCAATGCAAAGGTTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- gcttgct
- - - - - cactgga
- - - - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccactg